Selection and Evolution - Woozle Exercise

Readings

Introduction for students

This exercise focuses on the relative roles of chance and selection in the
evolutionary process. You should introduce yourself to the POPULUS program
that we will use during various parts of the course to demonstrate some
aspects of the evolutionary process. There is a short assignment using
the POPULUS simulations that you should complete and turn in next week.
The instructions below will lead you through accessing the program and completing
your assignment.

Exercise Instructions

Once In POPULUS
Read the Introduction!

From the Model menu go to Selection Models and select "Woozleology".
This is the demonstration Richard Dawkins discusses in the first part
of the reading. Be sure to read the introduction and make sure you know
how the program works. For an explanation of the Woozle demonstration,
go to the "Help" menu and find the folder for Selection Models -
open it and then open the Woozleology file and read the "Background"
information and "Parameters" information.

We will examine how aspects of brood size, mutation rate, and recombination
rate affect the time it takes to “select” the phrase “METHINKS IT IS LIKE
A WOOZLE”. Play around with the program examining the effects of
changing brood size, mutation rate, and recombination rate.

Homework

During discussion you will be assigned one of the following parameters
to examine:

BROOD SIZE this is the number of descendent copies from the original
phrase. The one phrase that is most similar to the target phrase will
be selected to be the parent phrase for the next generation.

Set mutation rate = 0.01; model a diploid, sexual process=
no

Run 3 simulations at each of the following brood sizes (15
total simulations): 2,10,50,100,500

Calculate the mean number of generations it takes to “evolve”
the phrase at each brood size.

MUTATION RATE this is the probability that a letter will change
or “mutate” to a different letter in the progeny of the parental phrase.

Set brood size = 50; model a diploid, sexual process=
no

Run 3 simulations at each of the following mutation rates (12
total simulations): 0.001, 0.01, 0.1, 0.2

Calculate the mean number of generations it takes to “evolve”
the phrase at each brood size.

RECOMBINATION FRACTION. In this simulation, two parent phrases
are selected; one from the first 25 progeny and another from the second
25. These phrases “recombine” to create progeny phrases. POPULUS draw 2
random numbers. The first is tested against the “recombination fraction.”
If it exceeds the recombination fraction, then there is no
recombination. If the number is less than the recombination fraction,
transcription switches to the other parent, and continues from that second
parent until another recombination “crossover” occurs. The second random
number determines whether the letter will mutate or not. You can view recombination
by selecting YES for SHOW RECOMBINATION?, but the program will take a very
long time. By pressing <esc> you can terminate the experiment.
For your experiments select NO and the program will run much more quickly.

Run 3 simulations at each of the following mutation rates (12
total simulations): 0, 0.1,0.25, 0.5

Calculate the mean number of generations it takes to “evolve”
the phrase at each brood size.

Graph the mean number of generations it takes to “evolve” the phrase
against the range of your parameter. Be prepared to discuss in class the
how and why changing your parameter affects the time it takes to evolve
the phrase.